Okay. It looks like what happens is that setuptools includes site.py as
site-patch.py. It then proceeds to install site.py for any package which
installs an egg. This includes setuptools itself; thus the site.py installation.
setuptools needs to install this site.py file because it relies on using .pth
files to add eggs into the path before site-packages (python's site.py only
allows appending to the path.)
Neal, does the setuptools site.py actually break anything?